rs10512085

Variant names:

• chr9-79309798-A-G
• rs10512085

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0711 in 152,190 control chromosomes in the GnomAD database, including 463 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (463 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10802 AN: 152072 Hom.: 456 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0509

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0711 AC: 10819 AN: 152190 Hom.: 463 Cov.: 32 AF XY: 0.0735 AC XY: 5467 AN XY: 74396

African (AFR) AF: 0.0484 AC: 2012 AN: 41542

American (AMR) AF: 0.111 AC: 1694 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.0510 AC: 263 AN: 5154

South Asian (SAS) AF: 0.136 AC: 654 AN: 4818

European-Finnish (FIN) AF: 0.128 AC: 1356 AN: 10594

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0665 AC: 4524 AN: 68008

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0679 Hom.: 673

Bravo AF: 0.0683

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.77
PhyloP100		-0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10512085; hg19: chr9-81924713;